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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ), 'gf_id' => 'HOM05D001085', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001085' ), 'data_identifier' => 'HOM05D001085', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001085', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '565', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p17150' => 'bna', 'A04p23360' => 'bna', 'A05p14870' => 'bna', 'A09p11690' => 'bna', 'A10p05330' => 'bna', 'Aa31LG5G6150' => 'aar', 'Actinidia04479' => 'ach', 'Actinidia05465' => 'ach', 'Actinidia08444' => 'ach', 'Actinidia21173' => 'ach', 'Actinidia21422' => 'ach', 'Actinidia24953' => 'ach', 'Actinidia27600' => 'ach', 'Actinidia31007' => 'ach', 'Actinidia40087' => 'ach', 'Ah.02g111670' => 'amhyb', 'Ah.02g113020' => 'amhyb', 'Ah.02g124530' => 'amhyb', 'Ah.11g048890' => 'amhyb', 'Ah.11g049920' => 'amhyb', 'AL1G16770' => 'aly', 'AL3G51200' => 'aly', 'AL4G25510' => 'aly', 'Aqoxy2G02077' => 'aox', 'Aqoxy2G03559' => 'aox', 'Aqoxy5G00322' => 'aox', 'Aqoxy5G01471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1UPR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2PL4QG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85J3HU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G0LEXN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I41NMG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y86I8S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHU8PA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4CKFD' => 'arhy', 'AT1G06760' => 'ath', 'AT2G18050' => 'ath', 'AT2G30620' => 'ath', 'ATR0147G002' => 'atr', 'ATR0665G275' => 'atr', 'ATR0684G112' => 'atr', 'ATR0706G126' => 'atr', 'ATR0767G007' => 'atr', 'Atru.chr3.779' => 'acertr', 'Atru.chr4.2231' => 'acertr', 'Atru.chr5.1599' => 'acertr', 'AUR62008327' => 'cqu', 'AUR62011923' => 'cqu', 'AUR62021770' => 'cqu', 'AUR62032238' => 'cqu', 'AUR62043236' => 'cqu', 'AUR62043610' => 'cqu', 'AUR62043714' => 'cqu', 'BcaB01g04085' => 'bca', 'BcaB02g06754' => 'bca', 'BcaB02g10336' => 'bca', 'BcaB06g28380' => 'bca', 'BcaB07g31694' => 'bca', 'BcaC01g06011' => 'bca', 'BcaC02g11158' => 'bca', 'BcaC04g22933' => 'bca', 'BcaC05g24647' => 'bca', 'BcaC07g42536' => 'bca', 'BcaNung06673' => 'bca', 'BolC3t14398H' => 'bol', 'BolC4t23526H' => 'bol', 'BolC4t27474H' => 'bol', 'BolC5t29264H' => 'bol', 'BolC9t54264H' => 'bol', 'BraA03t10989Z' => 'bra', 'BraA04t17864Z' => 'bra', 'BraA05t20414Z' => 'bra', 'BraA09t36814Z' => 'bra', 'BraA10t42797Z' => 'bra', 'C03p20240' => 'bna', 'C04p19880' => 'bna', 'C04p59660' => 'bna', 'C05p04920' => 'bna', 'C09p13750' => 'bna', 'CAN.G1007.14' => 'can', 'CAN.G1929.1' => 'can', 'CAN.G2049.5' => 'can', 'CAN.G6.4' => 'can', 'CAN.G771.17' => 'can', 'CAN.G99.14' => 'can', 'CANSAT01G0683' => 'cansat', 'CANSAT01G1516' => 'cansat', 'CANSAT54G0309' => 'cansat', 'CANSAT64G1069' => 'cansat', 'CARHR006440' => 'chi', 'CARHR006450' => 'chi', 'CARHR108540' => 'chi', 'CARHR124100' => 'chi', 'Carub.0001s0608' => 'cru', 'Carub.0003s3220' => 'cru', 'Carub.0004s1177' => 'cru', 'Ca_08653_v3' => 'car', 'Ca_09704_v3' => 'car', 'Ca_10038_v3' => 'car', 'Ca_24907_v3' => 'car', 'CBR_g21997' => 'cbr', 'CBR_g30681' => 'cbr', 'CBR_g30682' => 'cbr', 'Cc01_g18700' => 'ccan', 'Cc01_g21220' => 'ccan', 'Cc03_g04840' => 'ccan', 'Cc07_g10540' => 'ccan', 'CDE02G3280' => 'cde', 'CDE03G0285' => 'cde', 'CDE06G0431' => 'cde', 'CDE06G1540' => 'cde', 'CDE06G2369' => 'cde', 'CDE07G1752' => 'cde', 'Cfa005853' => 'cfa', 'Cfa006399' => 'cfa', 'Cfa006955' => 'cfa', 'Ciclev10005932m.g' => 'ccl', 'Ciclev10021453m.g' => 'ccl', 'Ciclev10026549m.g' => 'ccl', 'CiPaw.03G238200' => 'cil', 'CiPaw.04G183100' => 'cil', 'CiPaw.07G057100' => 'cil', 'CiPaw.07G114000' => 'cil', 'ClCG00G002230' => 'cla', 'ClCG01G020160' => 'cla', 'ClCG02G016780' => 'cla', 'ClCG07G000670' => 'cla', 'COL.COLO4_15379' => 'col', 'COL.COLO4_21935' => 'col', 'COL.COLO4_23281' => 'col', 'Cpa.g.c35527' => 'cpa', 'Cpa.g.sc1244.4' => 'cpa', 'Cpa.g.sc151.48' => 'cpa', 'Cpa.g.sc52.146' => 'cpa', 'Cpa.g.sc6.227' => 'cpa', 'Cre06.g275900' => 'cre', 'Cre13.g562300' => 'cre', 'Cre13.g567450' => 'cre', 'CsaV3_2G003970' => 'csa', 'CsaV3_6G036780' => 'csa', 'CsaV3_6G046960' => 'csa', 'CSS0007572' => 'camsi', 'CSS0018201' => 'camsi', 'CSS0023619' => 'camsi', 'CSS0026336' => 'camsi', 'CSS0032573' => 'camsi', 'CSS0048182' => 'camsi', 'DCAR_002352' => 'dca', 'DCAR_006647' => 'dca', 'DCAR_021495' => 'dca', 'DCAR_022197' => 'dca', 'DCAR_022199' => 'dca', 'DCAR_022202' => 'dca', 'DCAR_022204' => 'dca', 'DCAR_022206' => 'dca', 'DCAR_022208' => 'dca', 'DCAR_022210' => 'dca', 'DCAR_022212' => 'dca', 'DCAR_022214' => 'dca', 'DCAR_022216' => 'dca', 'DCAR_022219' => 'dca', 'DCAR_022221' => 'dca', 'DCAR_022223' => 'dca', 'DCAR_022225' => 'dca', 'DCAR_022239' => 'dca', 'DCAR_022241' => 'dca', 'DCAR_022283' => 'dca', 'DCAR_022284' => 'dca', 'DCAR_022285' => 'dca', 'DCAR_022286' => 'dca', 'DCAR_022287' => 'dca', 'DCAR_022288' => 'dca', 'DCAR_022289' => 'dca', 'DCAR_022290' => 'dca', 'DCAR_022291' => 'dca', 'DCAR_022292' => 'dca', 'DCAR_022293' => 'dca', 'DCAR_022294' => 'dca', 'DCAR_022295' => 'dca', 'DCAR_022296' => 'dca', 'DCAR_022297' => 'dca', 'DCAR_022298' => 'dca', 'Dinv01721' => 'din', 'Dinv03409' => 'din', 'Dinv10057' => 'din', 'Dinv20285' => 'din', 'Dinv22465' => 'din', 'Dinv33091' => 'din', 'Dinv33612' => 'din', 'Dinv34581' => 'din', 'Dinv44633' => 'din', 'Duzib106G1580' => 'dzi', 'Duzib138G1465' => 'dzi', 'Duzib138G1798' => 'dzi', 'Duzib147G0057' => 'dzi', 'Duzib177G0690' => 'dzi', 'Duzib187G1011' => 'dzi', 'Duzib211G0357' => 'dzi', 'Duzib264G1296' => 'dzi', 'ECA233G0351' => 'eca', 'ECA236G4256' => 'eca', 'ECA246G3604' => 'eca', 'ECA247G3217' => 'eca', 'EL10Ac5g10452' => 'bvu', 'EL10Ac5g10896' => 'bvu', 'EL10As8g23842' => 'bvu', 'Eucgr.H04318' => 'egr', 'Eucgr.I02364' => 'egr', 'Eucgr.K03300' => 'egr', 'FAN02G2181' => 'fan', 'FAN05G4505' => 'fan', 'FAN05G4996' => 'fan', 'FAN06G5105' => 'fan', 'FAN09G4528' => 'fan', 'FAN14G0915' => 'fan', 'FAN14G3295' => 'fan', 'FAN20G0964' => 'fan', 'FAN23G0173' => 'fan', 'FAN23G1625' => 'fan', 'FAN24G1558' => 'fan', 'FAN26G1623' => 'fan', 'FAN27G3035' => 'fan', 'FAN28G1748' => 'fan', 'FvH4_1g12030' => 'fve', 'FvH4_2g02381' => 'fve', 'FvH4_2g22280' => 'fve', 'FvH4_6g02630' => 'fve', 'FvH4_7g09410' => 'fve', 'Glyma.02G015100' => 'gma', 'Glyma.02G140900' => 'gma', 'Glyma.10G015700' => 'gma', 'Glyma.10G033100' => 'gma', 'Glyma.10G163300' => 'gma', 'Glyma.11G075500' => 'gma', 'Glyma.20G225900' => 'gma', 'Gohir.A08G061200' => 'ghi', 'Gohir.A11G127900' => 'ghi', 'Gohir.A11G176800' => 'ghi', 'Gohir.A13G169300' => 'ghi', 'Gohir.D08G070500' => 'ghi', 'Gohir.D11G117000' => 'ghi', 'Gohir.D11G133800' => 'ghi', 'Gohir.D11G184700' => 'ghi', 'Gohir.D13G174801' => 'ghi', 'Gorai.004G074200' => 'gra', 'Gorai.007G125300' => 'gra', 'Gorai.007G143000' => 'gra', 'Gorai.007G196300' => 'gra', 'Gorai.013G185800' => 'gra', 'GSVIVG01000755001' => 'vvi', 'GSVIVG01018114001' => 'vvi', 'GSVIVG01018807001' => 'vvi', 'GSVIVG01028074001' => 'vvi', 'GSVIVG01036230001' => 'vvi', 'HanXRQChr03g0069641' => 'han', 'HanXRQChr04g0113671' => 'han', 'HanXRQChr05g0153181' => 'han', 'HanXRQChr10g0281381' => 'han', 'HanXRQChr12g0386111' => 'han', 'HanXRQChr15g0468071' => 'han', 'HanXRQChr16g0531051' => 'han', 'Haze_03796' => 'cav', 'Haze_04378' => 'cav', 'Haze_04996' => 'cav', 'Haze_24548' => 'cav', 'Hma1.2p1_0120F.1_g056980' => 'hma', 'Hma1.2p1_0172F.1_g076290' => 'hma', 'Hma1.2p1_0187F.1_g081870' => 'hma', 'Hma1.2p1_0264F.1_g106140' => 'hma', 'Hma1.2p1_0276F.1_g111530' => 'hma', 'Hma1.2p1_0494F.1_g165610' => 'hma', 'Hma1.2p1_0684F.1_g203080' => 'hma', 'Hma1.2p1_0684F.1_g203081' => 'hma', 'Hma1.2p1_0743F.1_g211540' => 'hma', 'Hma1.2p1_0817F.1_g223185' => 'hma', 'Hma1.2p1_0863F.1_g230020' => 'hma', 'Hma1.2p1_0893F.1_g233460' => 'hma', 'Hma1.2p1_1029F.1_g249710' => 'hma', 'Hma1.2p1_1150F.1_g261790' => 'hma', 'Hma1.2p1_1193F.1_g265680' => 'hma', 'Hma1.2p1_2281F.1_g318730' => 'hma', 'Hma1.2p1_3307F.1_g335120' => 'hma', 'Hma1.2p1_3931F.1_g337990' => 'hma', 'HPP92_009686' => 'vpl', 'HPP92_014628' => 'vpl', 'HPP92_024333' => 'vpl', 'HPP92_024779' => 'vpl', 'Hund02687' => 'sun', 'Hund02890' => 'sun', 'Hund06183' => 'sun', 'Hund09379' => 'sun', 'Hund09576' => 'sun', 'Hund14037' => 'sun', 'Hund16483' => 'sun', 'Lalb_Chr01g0019811' => 'lal', 'Lalb_Chr02g0148911' => 'lal', 'Lalb_Chr02g0148921' => 'lal', 'Lalb_Chr06g0162611' => 'lal', 'Lalb_Chr21g0309421' => 'lal', 'Lalb_Chr21g0311031' => 'lal', 'Lj1A60T59' => 'lonja', 'Lj1g0014482' => 'lja', 'Lj1g0017141' => 'lja', 'Lj1g0021056' => 'lja', 'Lj2g0027402' => 'lja', 'Lj2P1156T38' => 'lonja', 'Lj2P1202T14' => 'lonja', 'Lj3C780T16' => 'lonja', 'Lj3C793T5' => 'lonja', 'Lj4A217T63' => 'lonja', 'Lj5g0015872' => 'lja', 'Lj5g0017035' => 'lja', 'Lj5g0019674' => 'lja', 'Lsat_1_v5_gn_1_16860' => 'lsa', 'Lsat_1_v5_gn_3_73941' => 'lsa', 'Lsat_1_v5_gn_4_117260' => 'lsa', 'Lsat_1_v5_gn_5_27201' => 'lsa', 'Lsat_1_v5_gn_5_72760' => 'lsa', 'Lsat_1_v5_gn_5_72780' => 'lsa', 'Lsat_1_v5_gn_8_91581' => 'lsa', 'Lsat_1_v5_gn_9_9661' => 'lsa', 'Manes.01G144600' => 'mes', 'Manes.01G224200' => 'mes', 'Manes.05G086000' => 'mes', 'Manes.08G136200' => 'mes', 'Manes.08G136300' => 'mes', 'Manes.15G036800' => 'mes', 'Mapoly0004s0232' => 'mpo', 'Mapoly0035s0095' => 'mpo', 'MBI05_g16281_MAGBIO' => 'mbi', 'MBI11_g24426_MAGBIO' => 'mbi', 'MBI18_g41097_MAGBIO' => 'mbi', 'MCO01G619' => 'mco', 'MCO01G620' => 'mco', 'MD01G1078700' => 'mdo', 'MD02G1134400' => 'mdo', 'MD04G1226600' => 'mdo', 'MD05G1204100' => 'mdo', 'MD10G1191200' => 'mdo', 'MD12G1243700' => 'mdo', 'MD15G1247400' => 'mdo', 'Medtr1g070390' => 'mtr', 'Medtr1g070435' => 'mtr', 'Medtr1g070440' => 'mtr', 'Medtr1g080700' => 'mtr', 'Medtr5g021730' => 'mtr', 'Medtr7g096280' => 'mtr', 'Medtr8g077160' => 'mtr', 'MELO3C004394.2' => 'cme', 'MELO3C007889.2' => 'cme', 'MELO3C014334.2' => 'cme', 'MELO3C028807.2' => 'cme', 'Migut.D00111' => 'egut', 'Migut.D00386' => 'egut', 'Migut.D00389' => 'egut', 'Migut.H01142' => 'egut', 'MSTRG.17478' => 'ama', 'MSTRG.18299' => 'ama', 'MSTRG.21662' => 'ama', 'MSTRG.23417' => 'ama', 'Nitab4.5_0000187g0330' => 'nta', 'Nitab4.5_0000525g0190' => 'nta', 'Nitab4.5_0001044g0080' => 'nta', 'Nitab4.5_0002880g0020' => 'nta', 'Nitab4.5_0004798g0020' => 'nta', 'Nitab4.5_0005721g0020' => 'nta', 'Nitab4.5_0006433g0010' => 'nta', 'Nitab4.5_0007897g0010' => 'nta', 'Nn1g02600' => 'nnu', 'Nn3g21605' => 'nnu', 'Nn4g26670' => 'nnu', 'Nn5g28646' => 'nnu', 'Nn5g29257' => 'nnu', 'Nn6g32266' => 'nnu', 'Oeu002283.2' => 'oeu', 'Oeu006462.1' => 'oeu', 'Oeu010121.1' => 'oeu', 'Oeu010122.1' => 'oeu', 'Oeu025800.1' => 'oeu', 'Oeu035302.1' => 'oeu', 'Oeu052134.1' => 'oeu', 'Oeu058808.1' => 'oeu', 'Os03g0799000' => 'osa', 'Os04g0253000' => 'osa', 'Os06g0130800' => 'osa', 'Os07g0184800' => 'osa', 'Peaxi162Scf00083g00822' => 'pax', 'Peaxi162Scf00100g00124' => 'pax', 'Peaxi162Scf00409g00614' => 'pax', 'Peaxi162Scf00813g00127' => 'pax', 'Peaxi162Scf01099g00002' => 'pax', 'Peaxi162Scf01530g00037' => 'pax', 'PGR004G1252' => 'pgr', 'PGR119G1296' => 'pgr', 'PGR119G1818' => 'pgr', 'PGR142G3271' => 'pgr', 'PGSC0003DMG400001127' => 'stu', 'PGSC0003DMG400003632' => 'stu', 'PGSC0003DMG400019910' => 'stu', 'PGSC0003DMG400020064' => 'stu', 'PGSC0003DMG400041021' => 'stu', 'Phvul.002G110800' => 'pvu', 'Phvul.007G178100' => 'pvu', 'Phvul.007G188400' => 'pvu', 'Phvul.007G216900' => 'pvu', 'Potri.002G043100' => 'ptr', 'Potri.002G199900' => 'ptr', 'Potri.005G116600' => 'ptr', 'Potri.005G219800' => 'ptr', 'Potri.007G014200' => 'ptr', 'Potri.008G162300' => 'ptr', 'Potri.010G076800' => 'ptr', 'Potri.013G042700' => 'ptr', 'Pp3c18_14270' => 'ppa', 'Pp3c18_19330' => 'ppa', 'Pp3c21_4670' => 'ppa', 'Pp3c21_7550' => 'ppa', 'Pp3c3_13380' => 'ppa', 'Pp3c5_3110' => 'ppa', 'Pp3c6_25560' => 'ppa', 'PRCOL_00004277' => 'pco', 'PRCOL_00004278' => 'pco', 'PRCOL_00004361' => 'pco', 'Prupe.6G345300' => 'ppe', 'Prupe.7G166400' => 'ppe', 'Prupe.8G230400' => 'ppe', 'Psat0s2070g0040' => 'psa', 'Psat2g060920' => 'psa', 'Psat2g126000' => 'psa', 'Psat2g126080' => 'psa', 'Psat3g037120' => 'psa', 'Psat3g060400' => 'psa', 'Psat4g132280' => 'psa', 'Psat6g056560' => 'psa', 'Psat6g056680' => 'psa', 'Psat6g056720' => 'psa', 'Psat6g056800' => 'psa', 'Psat6g056840' => 'psa', 'Psat6g056880' => 'psa', 'Psat6g056920' => 'psa', 'Psat6g057000' => 'psa', 'Psat6g144760' => 'psa', 'Psat7g021320' => 'psa', 'Psat7g144000' => 'psa', 'Psat7g193400' => 'psa', 'PSO017G2749' => 'pso', 'PSO063G6145' => 'pso', 'PSO081G0185' => 'pso', 'PSO173G0152' => 'pso', 'PSO357G0295' => 'pso', 'PSO384G1951' => 'pso', 'PSO541G0098' => 'pso', 'PSO541G1669' => 'pso', 'PSO541G1675' => 'pso', 'PSO541G4883' => 'pso', 'PSO675G0557' => 'pso', 'PSO675G2076' => 'pso', 'PSO675G2548' => 'pso', 'PSO675G3358' => 'pso', 'QL03p027650' => 'qlo', 'QL04p081392' => 'qlo', 'QL05p087639' => 'qlo', 'QL06p033694' => 'qlo', 'QL06p047903' => 'qlo', 'QL12p028821' => 'qlo', 'QL12p042916' => 'qlo', 'RcHm_v2.0_Chr2g0099661' => 'rch', 'RcHm_v2.0_Chr3g0450571' => 'rch', 'RcHm_v2.0_Chr6g0289241' => 'rch', 'Rhsim01G0268200' => 'rsi', 'Rhsim02G0033000' => 'rsi', 'Rhsim08G0034600' => 'rsi', 'Rhsim13G0031500' => 'rsi', 'Sabra02G0034900' => 'sbr', 'Sabra02G0158500' => 'sbr', 'Sabra05G0048600' => 'sbr', 'Sabra05G0095500' => 'sbr', 'Sabra05G0168700' => 'sbr', 'Sabra07G0011500' => 'sbr', 'Sabra08G0123800' => 'sbr', 'Sabra10G0032000' => 'sbr', 'Sabra13G0039100' => 'sbr', 'SalBow3G0813' => 'sbo', 'SalBow4G0849' => 'sbo', 'SalBow6G1422' => 'sbo', 'SalBow6G4641' => 'sbo', 'Sc03g0003560' => 'sci', 'Sc05g0000880' => 'sci', 'Sc13g0005010' => 'sci', 'Sc13g0006660' => 'sci', 'Sc13g0006700' => 'sci', 'Sed0000558' => 'sed', 'Sed0001934' => 'sed', 'Sed0014547' => 'sed', 'Sed0021901' => 'sed', 'Sed0026662' => 'sed', 'SEGI_13644' => 'sgi', 'SEGI_17769' => 'sgi', 'SEGI_19637' => 'sgi', 'SEGI_24183' => 'sgi', 'SEGI_24856' => 'sgi', 'SEGI_27341' => 'sgi', 'SEGI_33724' => 'sgi', 'SGA_v2.0_scaffold138G35265' => 'sas', 'SGA_v2.0_scaffold1G00572' => 'sas', 'SGA_v2.0_scaffold376G50259' => 'sas', 'SGA_v2.0_scaffold80G25783' => 'sas', 'SGA_v2.0_scaffold98G29329' => 'sas', 'SMO115G0235' => 'smo', 'SMO117G0284' => 'smo', 'SMO361G0804' => 'smo', 'Solyc02g084240.3' => 'sly', 'Solyc06g084020.4' => 'sly', 'Solyc09g066100.3' => 'sly', 'Solyc09g083380.4' => 'sly', 'Sopen02g028980' => 'spe', 'Sopen06g035400' => 'spe', 'Sopen09g027870' => 'spe', 'Sopen09g032300' => 'spe', 'Sp1g05490' => 'spa', 'Sp3g31490' => 'spa', 'Sp4g13160' => 'spa', 'TAR362G0199' => 'tar', 'TAR362G0743' => 'tar', 'TAR376G0470' => 'tar', 'TAR636G0899' => 'tar', 'THA.LOC104800806' => 'tha', 'THA.LOC104805824' => 'tha', 'THA.LOC104807487' => 'tha', 'THA.LOC104815834' => 'tha', 'THA.LOC104819761' => 'tha', 'THA.LOC104826253' => 'tha', 'Thecc.01G021400' => 'tca', 'Thecc.01G265500' => 'tca', 'Thecc.01G308400' => 'tca', 'Thecc.05G280600' => 'tca', 'Thhalv10008471m.g' => 'esa', 'Thhalv10017069m.g' => 'esa', 'Thhalv10022882m.g' => 'esa', 'TPR.G2400' => 'tpr', 'TPR.G30634' => 'tpr', 'TPR.G5712' => 'tpr', 'TPR.G9052' => 'tpr', 'TPR.G9056' => 'tpr', 'TWI09G1356' => 'twi', 'TWI12G0606' => 'twi', 'TWI12G0988' => 'twi', 'TWI18G0818' => 'twi', 'TWI73G0842' => 'twi', 'TWI75G0765' => 'twi', 'unitig_22.g5463' => 'ugi', 'unitig_8.g3891' => 'ugi', 'vmacro14861' => 'vma', 'vmacro18423' => 'vma', 'VMungo0464G1234' => 'vmu', 'VMungo0720G0785' => 'vmu', 'VMungo0720G1028' => 'vmu', 'VMungo0720G3130' => 'vmu', 'VMungo1215G0118' => 'vmu', 'Zm00001eb061060' => 'zma', 'Zm00001eb073400' => 'zma', 'Zm00001eb212820' => 'zma', 'Zm00001eb212840' => 'zma', 'Zm00001eb301680' => 'zma', 'Zm00001eb378280' => 'zma' ) $gf_id = 'HOM05D001085' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001085' ) $data_identifier = 'HOM05D001085' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 7, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 35, 'din' => (int) 9, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 18, 'vpl' => (int) 4, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 8, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 19, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 9, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb378280' $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